US military leaders have defended a key component of the military justice system which has been widely criticised amid growing concern at the way the armed services deal with cases of sexual assault.

Affording military commanders the "convening authority" – the ultimate power to nullify convictions by military juries – is necessary for "good order and discipline", military leaders told a Senate armed services committee hearing on Wednesday. It is the first time in 10 years that Congress has examined the issue of military sexual assault.

Senator Kirsten Gillibrand, the chair of the hearing, told a panel of judge advocate generals from the army, navy and air force that she was "extremely disturbed" by their answers.

The power of individual commanders to have final say on prosecutions has been thrown into the spotlight by a case at Aviano air base in Italy, in which the commander of the third air force, Lt General Craig Franklin, overturned the conviction for sexual assault of a senior fighter pilot last month. The case has fuelled concerns that the military does not do enough to protect members from sexual assault or act forcefully enough to prosecute offenders.

In a passionate exchange with the senior officers, during which Gillibrand cited 19,000 sexual assaults a year, with only 2,400 people coming forward because of fear, she questioned what constituted "good order and discipline". She told the Jags their actions to improve the military sexual abuse crisis was "not enough"

Gillibrand asked Harding which he believed had done their duty in the Aviano case – the jury or the convening authority. When he said both, she said: "Well one of the parties was wrong". Citing the testimony of the victim in the case, she said: "I can assure you she does not believe justice was done."

Senator Claire McCaskill, who has said she will offer legislation to strip US military commanders of power to overturn court-martial convictions in sexual-assault cases, told them: "If this amazing power given to one individual is about the good of the whole, it appears to me that Aviano general has failed."

The case, she said, had set the Air Force back "to Tailhook" – referring to a military scandal involving air force that happened in the 1990s.

Senators heard that typically a convening authority overturns convictions in a small percentage of cases.

Chuck Hagel, the new defense secretary told lawmakers this week that the Pentagon will review whether military commanders should continue to have the power to overturn such convictions.

Speaking after the hearing, Anu Bhagwati, executive director of Service Women's Action Network and former marine corps captain, said that removing the power of a convening authority from commanders was essential.

In response to the military testimony, Bhagwati, who also spoke at the hearing, said:"No doubt this issue is on the military's radar screen, but without a congressional change to the Uniform Code of Military Justice (UCMJ), the services are just moving the same pieces around the same chessboard.

"Only congressional reform that moves convening authority to prosecutors can serve as a game changer."

Under the UCMJ, a commander who convenes a court-martial is known as the convening authority and has the sole discretion to reduce or set aside guilty verdicts and sentences or to reverse a jury's verdict. Senators pointed out in the hearing that those convicted have the opportunity to appeal.

Earlier in the hearing, survivors of military sexual assaults told the senators that the military justice system was broken, riven with inherent bias, conflicts of interest and a hierarchical structure that ensured perpetrators of sexual assault went unpunished.

Victims said the system helped encourage predators in uniform, and urged senators to change the law to give survivors the same protections as civilians – namely an independent justice system.

Rebekah Havrilla, a former army sergeant who suffered post-traumatic stress disorder after being raped by another service member while in Afghanistan, told the Senate armed services committee that she found a "broken" criminal justice system.

Havrilla, who described an interview during the military investigation into her case as being the "most humiliating thing that I have ever experienced", said it was eventually closed after senior commanders decided not to pursue charges.

"What we need is a military with a fair and impartial criminal justice system, one that is run by professional and legal experts, not unit commanders," Havrilla said.

The US Department of Defense estimates that 86.5% of violent sexual crimes go unreported, of the approximately 19,000 that occur every year.

Brian Lewis, the first male survivor of military sexual abuse to testify before Congress, told lawmakers that sexual assault and rape was an "epidemic" in the military which remained untackled because of the existing reporting and prosecution system.

Lewis, who was raped by a non-commissioned officer on board a ship as a 20-year-old navy fire control technician, told lawmakers of the conflict of interest inherent in the system: "Service members must report rape to their commanders. However, if their commanders take action and prove that rape occurred, they also prove a failure of their own leadership."

Congress had, through laws like the Uniform Code of Military Justice, put commanders in charge of violent sexual crime, he said, but they had "failed to end this long-standing epidemic".

The decisions of commanders, he said, was why 86% of victims do not report abuse.

When asked by Gilibrand, the chair, if an independent prosecutor would have made a difference in his case, Lewis, who said he was a victim of a repeat sexual abuser, said: "I would have been able to get some form of justice."

He told the committee: "It feels like your heart breaks" when your commander tells not to report the abuse.

He told the committee that 56% of estimated victims of sexual assaults in the US military are men and 44% women, and urged them not to ignore men as the "invisible and ignored" survivors of military sexual trauma.

Nearly 2,500 sexual violence cases in the military services were reported in 2011, but only 240 made it to trial, Gillibrand said.

Brigette McCoy, a former army specialist and a Gulf war veteran, was 18 when she was raped, she told lawmakers. She did not report it, but three years later, she reported being sexually harassed by a different service member. This time, she filed a formal complaint, but got no official response.

"They did remove me from his team, and his formal apology consisted of him driving by me on base and saying 'sorry' out of his open car-door window," McCoy said.

She became suicidal and was made homeless – "two of the big issues in military sexual trauma" – after losing faith in the military chain of command, she said.

Had there been an independent system of prosecution, she said she would have pursued her case. "Ultimately I would still have my career. I would still have been serving, not fear for my life."

She urged the committee to act. "Let's not allow sexual predators who wear a uniform to become highly trained and decorated," she said. "Let's not just pluck a few leaves and trim the branch from the roots. Let's make it stop."

Lewis, who read from a statement of the victim in the Aviano case, said Franklin's decision was yet another example of an action that would have a "chilling effect" on military judges and prosecutors and could inhibit victims from coming forward.

The committee listened as victims and support groups spoke about the military culture that showed a "lack of understanding" about rape and sexual abuse.

Havrilla, who told the committee she was deployed 99% of the time as the only female, said: "the hostility is not towards women. The hostility is towards the feminine, towards the weak. It was not a gender issue. They are targeting what they see as less than."

She said that while she was well-treated and respected by some units, in others she found: "I can't tell you a single day that didn't go by without a rape joke or a sex joke. So in my mind it comes down to what was allowed by leaderships."